A digital scanning microscope usually makes a digital image of a sample such as a tissue sample placed in a microscope slide.
This is typically done by scanning the sample over the whole microscope slide and stitching different image bands together and/or by overlaying images measured at different wavelengths.
FIG. 1 schematically represents a cross-section of such a microscope slide. It notably comprises a glass slide 1 with a typical thickness of 1 mm (millimeter), a cover slip 2 with a typical thickness of 0.17 mm, a mounting medium 3 for fixing and sealing off a sample 4 like a tissue layer. The thickness of the sample 4 can typically be around 5 m, and for the mounting layer including the sample around 10 to 15 μm.
It is known, for example from WO2001084209, that digital scanning microscopes can comprise a 1D line sensor, also known as a line scan camera or as a linear array sensor. Such sensors comprise only one line, said differently one row, of sensing pixels. It is also known that compared to other types of sensors, like 2D array sensors for example, 1D line sensors are able to provide better continuous mechanical scanning operation, less stitching problems, and can allow for the use of so-called Time Delay Integration (TDI) line sensors.
In general, such 1D line sensors need to be combined with an efficient autofocus system in order to achieve good quality images of samples which position along the Z axis (depth direction) may vary of several microns (which can be more than the focal depth of the microscope). It is to be noted that such requirement is really important here, notably because the use of such sensors inherently requires a high number of scan increments during the image acquisition of the whole sample and thus involves an increase of focus adjustments during the scan.
In this respect, WO2001084209 discloses the most common solution known in the art which consists in generating and using a focus map. Such focus map provides measured optimum focus position to be used for the scanner objective in accordance with different scan positions along the scan path. The focus map is created prior to an actual image acquisition of the sample and made available for use any such acquisition process. During a scan process of acquiring the image of the sample, the focus position of the scanner objective is set on a trajectory that interpolates between the measured optimum focus positions.